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Trowel specifications

Information


Unique identifier OMICS_01111
Name Trowel
Software type Package/Module
Interface Command line interface
Restrictions to use None
Biological technology Illumina
Operating system Unix/Linux
Programming languages C++, Java
License GNU General Public License version 2.0
Computer skills Advanced
Stability Stable
Maintained Yes

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Maintainer


  • person_outline Detlef Weigel <>

Publication for Trowel

Trowel in publications

 (4)
PMCID: 5563063
PMID: 28821237
DOI: 10.1186/s12859-017-1784-8

[…] for illumina data, including ace [], bayeshammer [], bfc [], bless [], bless 2 [], blue [], ec [], fiona [], karect [], lighter [], musket [], pollux [], quake [], quorum [], racer [], sga-ec [] and trowel []. for a comprehensive overview of the characteristics of these ec tools and those for other sequencing platforms, we refer to []., the key idea is that the prior application of ec tools […]

PMCID: 4965716
PMID: 27461106
DOI: 10.1186/s40246-016-0068-0

[…] and to provide recommendations for users in selecting suitable methods with respect to specific ngs datasets., six k-spectrum-based methods, i.e., reptile, musket, bless, bloocoo, lighter, and trowel, were compared using six simulated sets of paired-end illumina sequencing data. these ngs datasets varied in coverage depth (10× to 120×), read length (36 to 100 bp), and genome size (4.6 […]

PMCID: 4624242
PMID: 26505996
DOI: 10.1371/journal.pone.0141369

[…] reads with a phred quality below q30 were filtered out using the fastx-toolkit (http://hannonlab.cshl.edu/fastx_toolkit/). additionally, to remove illlumina-specific sequencing errors, we applied trowel [], which is a k-mer spectrum-based error correction method for illumina reads, with default parameters., to obtain an accurate assembly and utilize the reference genome sequence, we performed […]

PMCID: 4719071
PMID: 26026159
DOI: 10.1093/bib/bbv029

[…] threshold), but creates its k-mer trust threshold for correction for each read separately. in this way, it adapts it to the local coverage and allows for k-mer coverage variations between reads.trowel [] does not use a coverage threshold for its k-mer spectrum at all. instead, it initially includes only k-mers whose bases all have quality values within the top 8% of the data set in at least […]


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Trowel institution(s)
Department of Molecular Biology, Max Planck Institute for Developmental Biology, Tübingen, Germany
Trowel funding source(s)
This work was supported by the Max Planck Society.

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